Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1680 to 1729 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
840 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Low confidence 201.924 196.817 1.02595
841 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 206.243 201.027
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] High confidence 198.781 190.66 1.04259
842 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Low confidence 206.244 201.028 1.02595
jm1 protein. [refseq;acc:nm_014008] High confidence 219.762 210.806 1.04248
843 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Low confidence 194.47 189.552 1.02595
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] High confidence 218.521 227.796 1.04244
844 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Low confidence 194.659 189.74 1.02592
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] High confidence 178.033 170.82 1.04223
845 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Low confidence 209.59 215.023 1.02592
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] High confidence 228.599 219.399 1.04193
846 forkhead box protein o1a (forkhead in rhabdomyosarcoma). [swissprot;acc:q12778] Low confidence 204.497 199.336 1.02589
methyltransferase like 2. [refseq;acc:nm_018396] High confidence 147.211 153.371 1.04184
847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Low confidence 203.643 198.505 1.02588
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] High confidence 147.211 153.371 1.04184
monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Low confidence 181.638 177.058 1.02587
849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] High confidence 147.211 153.371 1.04184
solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Low confidence 181.639 177.059 1.02587
850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] High confidence 107.842 112.329 1.04161
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Low confidence 197.337 192.361 1.02587
851 polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 203.191 198.072 1.02584
trs85 homolog. [swissprot;acc:q9y2l5] High confidence 107.842 112.329 1.04161
852 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 193.114 185.412 1.04154
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Low confidence 206.174 200.983 1.02583
853 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 199.788 194.759 1.02582
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] High confidence 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Low confidence 201.613 196.545 1.02579
855 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] 200.822 195.773
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] High confidence 178.514 171.42 1.04138
856 monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Low confidence 183.826 179.209 1.02576
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] High confidence 215.028 206.623 1.04068
857 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Low confidence 204.36 199.229 1.02575
putatative 28 kda protein. [refseq;acc:nm_020143] High confidence 227.241 236.467 1.0406
858 monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Low confidence 183.673 179.063 1.02575
syntaxin 12. [refseq;acc:nm_177424] High confidence 217.446 208.997 1.04043
859 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 1.04031
monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 183.611 179.004 1.02574
860 60s ribosomal protein l18a. [swissprot;acc:q02543] High confidence 234.025 224.958 1.04031
monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Low confidence 183.58 178.975 1.02573
861 40s ribosomal protein s19. [swissprot;acc:p39019] High confidence 234.025 224.958 1.04031
monocarboxylate transporter 5 (mct 5) (mct 4). [swissprot;acc:o15374] Low confidence 200.605 195.573 1.02573
862 60s ribosomal protein l31. [swissprot;acc:p12947] High confidence 234.025 224.958 1.04031
monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 183.625 179.018 1.02573
863 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] High confidence 240.194 230.957 1.03999
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Low confidence 202.981 197.889 1.02573
864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] High confidence 240.194 230.957 1.03999
monocarboxylate transporter 7 (mct 7) (mct 6). [swissprot;acc:o15403] Low confidence 200.605 195.573 1.02573
865 ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] 210.933 216.358 1.02572

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/